Multiple sequence alignment - TraesCS7D01G305300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G305300 chr7D 100.000 5508 0 0 1 5508 386760625 386755118 0.000000e+00 10172.0
1 TraesCS7D01G305300 chr7D 95.652 92 4 0 1519 1610 596233546 596233637 1.240000e-31 148.0
2 TraesCS7D01G305300 chr7A 94.239 3836 155 26 1602 5411 436789829 436786034 0.000000e+00 5799.0
3 TraesCS7D01G305300 chr7A 93.056 936 45 7 585 1520 436790743 436789828 0.000000e+00 1351.0
4 TraesCS7D01G305300 chr7A 95.960 99 2 2 1514 1611 301100419 301100516 5.710000e-35 159.0
5 TraesCS7D01G305300 chr7A 96.809 94 2 1 1519 1612 9539770 9539678 7.390000e-34 156.0
6 TraesCS7D01G305300 chr7A 100.000 28 0 0 1022 1049 321046358 321046331 1.000000e-02 52.8
7 TraesCS7D01G305300 chr7B 93.773 2409 103 13 1602 3990 381838371 381835990 0.000000e+00 3574.0
8 TraesCS7D01G305300 chr7B 92.776 1412 64 13 4022 5411 381835990 381834595 0.000000e+00 2008.0
9 TraesCS7D01G305300 chr7B 88.284 1562 102 37 3 1520 381839894 381838370 0.000000e+00 1796.0
10 TraesCS7D01G305300 chr7B 96.842 95 2 1 1519 1613 482820126 482820033 2.050000e-34 158.0
11 TraesCS7D01G305300 chr7B 89.623 106 11 0 5403 5508 707107889 707107994 9.620000e-28 135.0
12 TraesCS7D01G305300 chr7B 89.189 74 7 1 5158 5231 741941064 741940992 2.110000e-14 91.6
13 TraesCS7D01G305300 chr2D 77.891 294 58 6 136 423 367853917 367854209 5.670000e-40 176.0
14 TraesCS7D01G305300 chr5D 97.826 92 2 0 1512 1603 201522885 201522976 5.710000e-35 159.0
15 TraesCS7D01G305300 chr5D 97.849 93 1 1 1512 1603 565714530 565714438 5.710000e-35 159.0
16 TraesCS7D01G305300 chr5A 96.842 95 2 1 1517 1611 76742178 76742085 2.050000e-34 158.0
17 TraesCS7D01G305300 chr5A 73.515 404 75 19 70 451 367800361 367800754 2.080000e-24 124.0
18 TraesCS7D01G305300 chr6B 92.453 106 4 4 1516 1620 546656570 546656672 1.240000e-31 148.0
19 TraesCS7D01G305300 chr4A 91.071 112 4 5 1519 1629 537598005 537597899 4.450000e-31 147.0
20 TraesCS7D01G305300 chr4A 92.708 96 7 0 5413 5508 450604375 450604280 7.440000e-29 139.0
21 TraesCS7D01G305300 chr1B 93.750 96 6 0 5413 5508 360422843 360422748 1.600000e-30 145.0
22 TraesCS7D01G305300 chr1B 91.919 99 8 0 5410 5508 213081503 213081601 7.440000e-29 139.0
23 TraesCS7D01G305300 chr6A 91.919 99 8 0 5410 5508 499072706 499072804 7.440000e-29 139.0
24 TraesCS7D01G305300 chr4D 91.919 99 8 0 5410 5508 441684562 441684660 7.440000e-29 139.0
25 TraesCS7D01G305300 chr4D 100.000 28 0 0 3551 3578 489470468 489470495 1.000000e-02 52.8
26 TraesCS7D01G305300 chr2B 91.919 99 8 0 5410 5508 551567869 551567967 7.440000e-29 139.0
27 TraesCS7D01G305300 chr2B 91.919 99 8 0 5410 5508 725915229 725915327 7.440000e-29 139.0
28 TraesCS7D01G305300 chr1A 92.708 96 7 0 5413 5508 466559926 466559831 7.440000e-29 139.0
29 TraesCS7D01G305300 chr5B 82.609 69 8 3 5178 5244 558707492 558707426 2.140000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G305300 chr7D 386755118 386760625 5507 True 10172.000000 10172 100.0000 1 5508 1 chr7D.!!$R1 5507
1 TraesCS7D01G305300 chr7A 436786034 436790743 4709 True 3575.000000 5799 93.6475 585 5411 2 chr7A.!!$R3 4826
2 TraesCS7D01G305300 chr7B 381834595 381839894 5299 True 2459.333333 3574 91.6110 3 5411 3 chr7B.!!$R3 5408

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
923 966 0.034337 TCCTCGTGTTAAGCCACCAC 59.966 55.0 0.0 0.0 31.47 4.16 F
1781 1833 0.251916 CCGCCTCCACATACTTTGGA 59.748 55.0 0.0 0.0 41.06 3.53 F
2379 2446 0.618458 GGGCAGAGGTATGTGTGGAA 59.382 55.0 0.0 0.0 0.00 3.53 F
3496 3581 0.108945 GATGTGGAAAAGCAGGCAGC 60.109 55.0 0.0 0.0 46.19 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2144 1.073216 CGCTTGTAGTGCTCCGTCAG 61.073 60.000 0.0 0.0 0.00 3.51 R
3489 3574 1.538047 TTTTCCTGCTTAGCTGCCTG 58.462 50.000 5.6 0.0 0.00 4.85 R
4045 4133 3.066760 GTGGTTACTTGCAGCCAATATCC 59.933 47.826 0.0 0.0 29.81 2.59 R
5387 5502 0.174845 TGATTCCAAGTACGGCTCGG 59.825 55.000 0.0 0.0 0.00 4.63 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.767665 TCCAGAAAAAGCAATACAAGCAGTA 59.232 36.000 0.00 0.00 37.06 2.74
37 38 4.400251 AGCAATACAAGCAGTACTACGGTA 59.600 41.667 0.00 0.00 35.05 4.02
38 39 4.501921 GCAATACAAGCAGTACTACGGTAC 59.498 45.833 0.00 0.00 46.18 3.34
58 59 9.336171 ACGGTACTTTTTCCTAGATAGTAGTAG 57.664 37.037 0.00 0.00 0.00 2.57
65 66 9.917887 TTTTTCCTAGATAGTAGTAGTACTGCT 57.082 33.333 22.30 22.30 43.57 4.24
83 84 2.880268 TGCTGCGGAATATCCATTTCTG 59.120 45.455 0.00 0.00 35.91 3.02
92 93 6.519721 CGGAATATCCATTTCTGAGTCCAGAT 60.520 42.308 0.00 0.00 41.91 2.90
104 105 1.211457 AGTCCAGATTCATCAGCACCC 59.789 52.381 0.00 0.00 0.00 4.61
114 115 0.107508 ATCAGCACCCGGTCAAGATG 60.108 55.000 0.00 0.00 0.00 2.90
115 116 1.003355 CAGCACCCGGTCAAGATGT 60.003 57.895 0.00 0.00 0.00 3.06
116 117 0.606401 CAGCACCCGGTCAAGATGTT 60.606 55.000 0.00 0.00 0.00 2.71
194 196 4.953269 CGTGAGTGCGCTTTAAATTTAGA 58.047 39.130 9.73 0.00 0.00 2.10
195 197 5.560148 CGTGAGTGCGCTTTAAATTTAGAT 58.440 37.500 9.73 0.00 0.00 1.98
255 258 2.790433 TGGGCCAGAACAGACATAAAC 58.210 47.619 0.00 0.00 0.00 2.01
256 259 2.092323 GGGCCAGAACAGACATAAACC 58.908 52.381 4.39 0.00 0.00 3.27
262 265 5.123344 GCCAGAACAGACATAAACCGTAAAT 59.877 40.000 0.00 0.00 0.00 1.40
270 273 9.667989 ACAGACATAAACCGTAAATGTTTTTAC 57.332 29.630 0.00 0.00 42.44 2.01
285 288 6.712179 TGTTTTTACGGACCCTAAATTTGT 57.288 33.333 0.00 0.00 0.00 2.83
287 290 6.546772 TGTTTTTACGGACCCTAAATTTGTCT 59.453 34.615 0.00 0.00 0.00 3.41
316 319 6.782082 ACATAGAGCTACTCAGATGTTCAA 57.218 37.500 8.52 0.00 36.56 2.69
317 320 7.175347 ACATAGAGCTACTCAGATGTTCAAA 57.825 36.000 8.52 0.00 36.56 2.69
318 321 7.790027 ACATAGAGCTACTCAGATGTTCAAAT 58.210 34.615 8.52 0.00 36.56 2.32
319 322 8.918116 ACATAGAGCTACTCAGATGTTCAAATA 58.082 33.333 8.52 0.00 36.56 1.40
324 327 9.973450 GAGCTACTCAGATGTTCAAATAATCTA 57.027 33.333 0.00 0.00 0.00 1.98
362 365 4.982295 TCTCACGCACCAAATTATCTATCG 59.018 41.667 0.00 0.00 0.00 2.92
365 370 6.452242 TCACGCACCAAATTATCTATCGTAT 58.548 36.000 0.00 0.00 0.00 3.06
368 373 8.705134 CACGCACCAAATTATCTATCGTATAAA 58.295 33.333 0.00 0.00 0.00 1.40
470 505 1.904537 TGATCACATGAGCAGTGGAGT 59.095 47.619 0.00 0.00 35.30 3.85
471 506 3.099141 TGATCACATGAGCAGTGGAGTA 58.901 45.455 0.00 0.00 35.30 2.59
472 507 3.131755 TGATCACATGAGCAGTGGAGTAG 59.868 47.826 0.00 0.00 35.30 2.57
473 508 1.205655 TCACATGAGCAGTGGAGTAGC 59.794 52.381 0.00 0.00 37.58 3.58
474 509 1.066645 CACATGAGCAGTGGAGTAGCA 60.067 52.381 0.00 0.00 33.43 3.49
475 510 1.206610 ACATGAGCAGTGGAGTAGCAG 59.793 52.381 0.00 0.00 0.00 4.24
476 511 1.206610 CATGAGCAGTGGAGTAGCAGT 59.793 52.381 0.00 0.00 0.00 4.40
487 522 0.036306 AGTAGCAGTTTTCCCCGTGG 59.964 55.000 0.00 0.00 0.00 4.94
497 532 0.320946 TTCCCCGTGGTTTCGTGATC 60.321 55.000 0.00 0.00 0.00 2.92
498 533 1.189524 TCCCCGTGGTTTCGTGATCT 61.190 55.000 0.00 0.00 0.00 2.75
499 534 1.019278 CCCCGTGGTTTCGTGATCTG 61.019 60.000 0.00 0.00 0.00 2.90
500 535 1.635663 CCCGTGGTTTCGTGATCTGC 61.636 60.000 0.00 0.00 0.00 4.26
516 551 6.221659 GTGATCTGCATGAAGTGATGAGATA 58.778 40.000 0.00 0.00 0.00 1.98
517 552 6.704937 GTGATCTGCATGAAGTGATGAGATAA 59.295 38.462 0.00 0.00 0.00 1.75
525 560 7.649057 CATGAAGTGATGAGATAACATGCAAT 58.351 34.615 0.00 0.00 0.00 3.56
541 576 7.600231 ACATGCAATATGTGATTGGGATAAA 57.400 32.000 0.00 0.00 0.00 1.40
552 587 6.015519 TGTGATTGGGATAAACAAGTCAAAGG 60.016 38.462 0.00 0.00 0.00 3.11
553 588 4.864704 TTGGGATAAACAAGTCAAAGGC 57.135 40.909 0.00 0.00 0.00 4.35
554 589 4.112634 TGGGATAAACAAGTCAAAGGCT 57.887 40.909 0.00 0.00 0.00 4.58
555 590 4.079253 TGGGATAAACAAGTCAAAGGCTC 58.921 43.478 0.00 0.00 0.00 4.70
556 591 3.444034 GGGATAAACAAGTCAAAGGCTCC 59.556 47.826 0.00 0.00 0.00 4.70
557 592 4.079253 GGATAAACAAGTCAAAGGCTCCA 58.921 43.478 0.00 0.00 0.00 3.86
648 683 2.738521 GAGCGCGGACACACACAT 60.739 61.111 8.83 0.00 0.00 3.21
666 701 4.433615 CACATACAGTGCCCTACTACAAG 58.566 47.826 0.00 0.00 42.15 3.16
730 770 0.911769 CACCTAGATCTTGTGGGCCA 59.088 55.000 0.00 0.00 0.00 5.36
733 773 2.975489 ACCTAGATCTTGTGGGCCATAG 59.025 50.000 10.70 11.06 0.00 2.23
740 780 2.170607 TCTTGTGGGCCATAGCTTAGAC 59.829 50.000 10.70 0.00 39.73 2.59
741 781 1.879575 TGTGGGCCATAGCTTAGACT 58.120 50.000 10.70 0.00 39.73 3.24
811 851 3.841353 CCCTCCCGTAGCCCCCTA 61.841 72.222 0.00 0.00 0.00 3.53
819 859 1.076044 GTAGCCCCCTACCGGTACA 60.076 63.158 11.16 0.00 38.38 2.90
837 877 3.625897 CCAGGCTCACGTGTCCCA 61.626 66.667 22.63 2.71 0.00 4.37
838 878 2.357517 CAGGCTCACGTGTCCCAC 60.358 66.667 22.63 9.30 0.00 4.61
839 879 2.524394 AGGCTCACGTGTCCCACT 60.524 61.111 22.63 11.04 31.34 4.00
840 880 2.048127 GGCTCACGTGTCCCACTC 60.048 66.667 16.51 0.00 31.34 3.51
841 881 2.048127 GCTCACGTGTCCCACTCC 60.048 66.667 16.51 0.00 31.34 3.85
842 882 2.574955 GCTCACGTGTCCCACTCCT 61.575 63.158 16.51 0.00 31.34 3.69
922 965 0.320374 CTCCTCGTGTTAAGCCACCA 59.680 55.000 0.00 0.00 31.47 4.17
923 966 0.034337 TCCTCGTGTTAAGCCACCAC 59.966 55.000 0.00 0.00 31.47 4.16
924 967 0.953960 CCTCGTGTTAAGCCACCACC 60.954 60.000 0.00 0.00 31.47 4.61
977 1020 3.814504 TCATCCCTGCCTTCTTTCTTT 57.185 42.857 0.00 0.00 0.00 2.52
978 1021 3.690460 TCATCCCTGCCTTCTTTCTTTC 58.310 45.455 0.00 0.00 0.00 2.62
1376 1428 2.562635 CTGAGGATCTGGTGCATTCAG 58.437 52.381 12.18 12.18 34.92 3.02
1401 1453 5.984233 TTGTGCGATTCATGGTATTAGAC 57.016 39.130 0.00 0.00 0.00 2.59
1512 1564 2.341168 GCGTGTATTGCCGTTTGATTTG 59.659 45.455 0.00 0.00 0.00 2.32
1515 1567 4.856487 CGTGTATTGCCGTTTGATTTGATT 59.144 37.500 0.00 0.00 0.00 2.57
1519 1571 9.509855 GTGTATTGCCGTTTGATTTGATTATTA 57.490 29.630 0.00 0.00 0.00 0.98
1520 1572 9.509855 TGTATTGCCGTTTGATTTGATTATTAC 57.490 29.630 0.00 0.00 0.00 1.89
1521 1573 9.730420 GTATTGCCGTTTGATTTGATTATTACT 57.270 29.630 0.00 0.00 0.00 2.24
1522 1574 8.856490 ATTGCCGTTTGATTTGATTATTACTC 57.144 30.769 0.00 0.00 0.00 2.59
1523 1575 6.791303 TGCCGTTTGATTTGATTATTACTCC 58.209 36.000 0.00 0.00 0.00 3.85
1524 1576 6.183360 TGCCGTTTGATTTGATTATTACTCCC 60.183 38.462 0.00 0.00 0.00 4.30
1525 1577 6.039382 GCCGTTTGATTTGATTATTACTCCCT 59.961 38.462 0.00 0.00 0.00 4.20
1526 1578 7.639945 CCGTTTGATTTGATTATTACTCCCTC 58.360 38.462 0.00 0.00 0.00 4.30
1527 1579 7.499232 CCGTTTGATTTGATTATTACTCCCTCT 59.501 37.037 0.00 0.00 0.00 3.69
1528 1580 8.338259 CGTTTGATTTGATTATTACTCCCTCTG 58.662 37.037 0.00 0.00 0.00 3.35
1529 1581 9.178758 GTTTGATTTGATTATTACTCCCTCTGT 57.821 33.333 0.00 0.00 0.00 3.41
1545 1597 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
1547 1599 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
1597 1649 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
1598 1650 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
1599 1651 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
1600 1652 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
1601 1653 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
1606 1658 6.651975 ATTAGTTTACGGAGGGAGTATCTG 57.348 41.667 0.00 0.00 33.73 2.90
1642 1694 2.380064 AGGAGGTTTGCCATGTTTCA 57.620 45.000 0.00 0.00 37.19 2.69
1781 1833 0.251916 CCGCCTCCACATACTTTGGA 59.748 55.000 0.00 0.00 41.06 3.53
1832 1884 1.365633 GCGCCGATCAGAGAGGAAT 59.634 57.895 0.00 0.00 0.00 3.01
1874 1940 5.782047 CCTTTTGTGTATGGAATCAAAGCA 58.218 37.500 0.00 0.00 32.67 3.91
1933 2000 6.714810 TGCCCTGTAATCAAGCGAATAAATAT 59.285 34.615 0.00 0.00 0.00 1.28
2241 2308 1.699054 TTGCTGAGACTGGTGCTGGT 61.699 55.000 0.00 0.00 0.00 4.00
2283 2350 1.525995 AGTGTGTGCTCGGTTTGGG 60.526 57.895 0.00 0.00 0.00 4.12
2375 2442 0.620556 CTTGGGGCAGAGGTATGTGT 59.379 55.000 0.00 0.00 0.00 3.72
2379 2446 0.618458 GGGCAGAGGTATGTGTGGAA 59.382 55.000 0.00 0.00 0.00 3.53
3011 3082 6.597672 CAGTGCTGGGTAAGTATTTTGATGTA 59.402 38.462 0.00 0.00 0.00 2.29
3205 3284 7.606456 TCTCTACCATTTATGTTTCCTTGTCAC 59.394 37.037 0.00 0.00 0.00 3.67
3270 3349 7.330208 CAGTTGATTTTCATCCAATTGACTTCC 59.670 37.037 7.12 0.00 0.00 3.46
3286 3365 6.282199 TGACTTCCAGTCCATCTACTAAAC 57.718 41.667 1.46 0.00 44.44 2.01
3360 3445 1.880027 CAAGTCTGTGGTTTAGGCACC 59.120 52.381 0.00 0.00 37.34 5.01
3387 3472 5.005779 CGCTGGTCTAGATTTACATGTGAAC 59.994 44.000 9.11 0.00 0.00 3.18
3429 3514 6.655425 AGGCATTACTGAAGGTTAAAACTCTC 59.345 38.462 0.00 0.00 0.00 3.20
3449 3534 7.754625 ACTCTCGAGATAGTAAGTTTCAGTTC 58.245 38.462 17.03 0.00 0.00 3.01
3496 3581 0.108945 GATGTGGAAAAGCAGGCAGC 60.109 55.000 0.00 0.00 46.19 5.25
3585 3673 9.442047 GATTATCTTAATCCACCTTGATACCAG 57.558 37.037 0.00 0.00 0.00 4.00
3592 3680 4.422057 TCCACCTTGATACCAGACACTAA 58.578 43.478 0.00 0.00 0.00 2.24
3599 3687 8.603304 ACCTTGATACCAGACACTAATTAAGTT 58.397 33.333 0.00 0.00 35.76 2.66
3639 3727 7.373966 TGTTTTAAAACGTTCTGAATCGTTAGC 59.626 33.333 22.57 13.45 46.95 3.09
3672 3760 1.068588 ACTGACTAAGTCTGCAACGCA 59.931 47.619 0.00 0.00 31.64 5.24
3677 3765 4.752604 TGACTAAGTCTGCAACGCAAAATA 59.247 37.500 0.00 0.00 38.41 1.40
3693 3781 5.164002 CGCAAAATAAATGGCAAACACTACC 60.164 40.000 0.00 0.00 0.00 3.18
3695 3783 7.093992 GCAAAATAAATGGCAAACACTACCTA 58.906 34.615 0.00 0.00 0.00 3.08
3720 3808 6.109359 AGGCATCTGAAAGTGACTGTATTAC 58.891 40.000 0.00 0.00 33.12 1.89
3725 3813 9.208022 CATCTGAAAGTGACTGTATTACAGAAA 57.792 33.333 26.58 13.22 41.44 2.52
3780 3868 3.408634 TGCTAGCTTGTAAACCTTCACC 58.591 45.455 17.23 0.00 0.00 4.02
3783 3871 2.490991 AGCTTGTAAACCTTCACCGAC 58.509 47.619 0.00 0.00 0.00 4.79
3792 3880 8.314143 TGTAAACCTTCACCGACTAATTTTAG 57.686 34.615 0.00 0.00 36.82 1.85
3813 3901 4.445452 GACACATGGTCAATTGCAATCT 57.555 40.909 13.38 0.20 46.19 2.40
3814 3902 4.813027 GACACATGGTCAATTGCAATCTT 58.187 39.130 13.38 0.00 46.19 2.40
3815 3903 4.562082 ACACATGGTCAATTGCAATCTTG 58.438 39.130 13.38 9.45 0.00 3.02
3816 3904 3.930229 CACATGGTCAATTGCAATCTTGG 59.070 43.478 13.38 3.34 0.00 3.61
3817 3905 3.833650 ACATGGTCAATTGCAATCTTGGA 59.166 39.130 13.38 5.73 0.00 3.53
3818 3906 4.468510 ACATGGTCAATTGCAATCTTGGAT 59.531 37.500 13.38 0.05 0.00 3.41
3861 3949 6.931838 TGTAGGAGAGAAATAACACGTGATT 58.068 36.000 25.01 14.90 0.00 2.57
4045 4133 5.068234 ACATGCTTGATGTTTCCATCTTG 57.932 39.130 6.60 0.00 43.20 3.02
4234 4342 2.837591 TGTCTTAAGCCTGCTGGTGATA 59.162 45.455 11.69 0.00 35.27 2.15
4297 4405 2.050144 CCCCCTGTCATGTATGCTACT 58.950 52.381 0.00 0.00 0.00 2.57
4298 4406 3.239449 CCCCCTGTCATGTATGCTACTA 58.761 50.000 0.00 0.00 0.00 1.82
4299 4407 3.006967 CCCCCTGTCATGTATGCTACTAC 59.993 52.174 0.00 0.00 0.00 2.73
4390 4499 2.659063 CCTGGAGACATCCCACGCA 61.659 63.158 0.00 0.00 46.04 5.24
4429 4538 4.947147 TGCCCAACACTGCCGGAC 62.947 66.667 5.05 0.00 0.00 4.79
4601 4710 4.215613 GCTTAGTGTTGTTCTTTGGGGTAG 59.784 45.833 0.00 0.00 0.00 3.18
4725 4834 4.800784 TGGTAAATAAAGGCTCGTTTTGC 58.199 39.130 0.00 0.00 0.00 3.68
4784 4893 4.624015 CCTTGTGATGATTTTGCTGTGTT 58.376 39.130 0.00 0.00 0.00 3.32
4785 4894 4.446385 CCTTGTGATGATTTTGCTGTGTTG 59.554 41.667 0.00 0.00 0.00 3.33
4786 4895 4.915158 TGTGATGATTTTGCTGTGTTGA 57.085 36.364 0.00 0.00 0.00 3.18
4851 4963 2.031120 TGCTGCCTATAATTGCAACCC 58.969 47.619 0.00 0.00 36.98 4.11
4937 5049 3.618351 ACTGAGATTGCAATCTTCCAGG 58.382 45.455 36.67 27.53 45.39 4.45
5107 5219 1.383109 ATCGCAGGGACAGGGATGA 60.383 57.895 0.00 0.00 44.93 2.92
5187 5302 6.209192 TGAAATGTCATGGCAGTACAAAGAAT 59.791 34.615 6.04 0.00 0.00 2.40
5232 5347 6.153000 ACATTCAAGTTCGTAGACCATCTAGT 59.847 38.462 0.00 0.00 34.32 2.57
5235 5350 5.886474 TCAAGTTCGTAGACCATCTAGTGAT 59.114 40.000 0.00 0.00 34.32 3.06
5241 5356 7.012138 GTTCGTAGACCATCTAGTGATGACTAA 59.988 40.741 7.51 0.00 44.71 2.24
5351 5466 7.886338 AGTTAGAAAACTGCTAAATTTCCAGG 58.114 34.615 17.87 2.90 44.40 4.45
5386 5501 0.533032 GCTCTCGGCTGGACTTTACT 59.467 55.000 0.00 0.00 38.06 2.24
5387 5502 1.470112 GCTCTCGGCTGGACTTTACTC 60.470 57.143 0.00 0.00 38.06 2.59
5388 5503 1.135333 CTCTCGGCTGGACTTTACTCC 59.865 57.143 0.00 0.00 0.00 3.85
5394 5509 0.179134 CTGGACTTTACTCCGAGCCG 60.179 60.000 0.00 0.00 32.22 5.52
5411 5526 3.039011 AGCCGTACTTGGAATCACCTAT 58.961 45.455 0.00 0.00 39.86 2.57
5412 5527 3.454812 AGCCGTACTTGGAATCACCTATT 59.545 43.478 0.00 0.00 39.86 1.73
5413 5528 3.808174 GCCGTACTTGGAATCACCTATTC 59.192 47.826 0.00 0.00 42.90 1.75
5421 5536 3.133141 GAATCACCTATTCCCTCTGCC 57.867 52.381 0.00 0.00 38.47 4.85
5422 5537 1.439543 ATCACCTATTCCCTCTGCCC 58.560 55.000 0.00 0.00 0.00 5.36
5423 5538 1.048724 TCACCTATTCCCTCTGCCCG 61.049 60.000 0.00 0.00 0.00 6.13
5424 5539 1.766461 ACCTATTCCCTCTGCCCGG 60.766 63.158 0.00 0.00 0.00 5.73
5425 5540 1.459539 CCTATTCCCTCTGCCCGGA 60.460 63.158 0.73 0.00 0.00 5.14
5426 5541 1.054406 CCTATTCCCTCTGCCCGGAA 61.054 60.000 0.73 0.00 42.24 4.30
5427 5542 0.837272 CTATTCCCTCTGCCCGGAAA 59.163 55.000 0.73 0.00 41.39 3.13
5428 5543 1.421646 CTATTCCCTCTGCCCGGAAAT 59.578 52.381 0.73 0.00 41.39 2.17
5429 5544 1.518367 ATTCCCTCTGCCCGGAAATA 58.482 50.000 0.73 0.00 41.39 1.40
5430 5545 0.544697 TTCCCTCTGCCCGGAAATAC 59.455 55.000 0.73 0.00 35.19 1.89
5431 5546 0.326238 TCCCTCTGCCCGGAAATACT 60.326 55.000 0.73 0.00 0.00 2.12
5432 5547 0.546598 CCCTCTGCCCGGAAATACTT 59.453 55.000 0.73 0.00 0.00 2.24
5433 5548 1.668419 CCTCTGCCCGGAAATACTTG 58.332 55.000 0.73 0.00 0.00 3.16
5434 5549 1.065418 CCTCTGCCCGGAAATACTTGT 60.065 52.381 0.73 0.00 0.00 3.16
5435 5550 2.280628 CTCTGCCCGGAAATACTTGTC 58.719 52.381 0.73 0.00 0.00 3.18
5436 5551 1.626321 TCTGCCCGGAAATACTTGTCA 59.374 47.619 0.73 0.00 0.00 3.58
5437 5552 2.238646 TCTGCCCGGAAATACTTGTCAT 59.761 45.455 0.73 0.00 0.00 3.06
5438 5553 2.614057 CTGCCCGGAAATACTTGTCATC 59.386 50.000 0.73 0.00 0.00 2.92
5439 5554 2.026729 TGCCCGGAAATACTTGTCATCA 60.027 45.455 0.73 0.00 0.00 3.07
5440 5555 3.013921 GCCCGGAAATACTTGTCATCAA 58.986 45.455 0.73 0.00 0.00 2.57
5441 5556 3.442273 GCCCGGAAATACTTGTCATCAAA 59.558 43.478 0.73 0.00 32.87 2.69
5442 5557 4.082463 GCCCGGAAATACTTGTCATCAAAA 60.082 41.667 0.73 0.00 32.87 2.44
5443 5558 5.394115 GCCCGGAAATACTTGTCATCAAAAT 60.394 40.000 0.73 0.00 32.87 1.82
5444 5559 6.183360 GCCCGGAAATACTTGTCATCAAAATA 60.183 38.462 0.73 0.00 32.87 1.40
5445 5560 7.417612 CCCGGAAATACTTGTCATCAAAATAG 58.582 38.462 0.73 0.00 32.87 1.73
5446 5561 7.282224 CCCGGAAATACTTGTCATCAAAATAGA 59.718 37.037 0.73 0.00 32.87 1.98
5447 5562 8.840321 CCGGAAATACTTGTCATCAAAATAGAT 58.160 33.333 0.00 0.00 32.87 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.498570 TGCTTGTATTGCTTTTTCTGGAAAATT 59.501 29.630 8.96 0.00 39.69 1.82
4 5 5.068987 ACTGCTTGTATTGCTTTTTCTGGAA 59.931 36.000 0.00 0.00 0.00 3.53
5 6 4.584325 ACTGCTTGTATTGCTTTTTCTGGA 59.416 37.500 0.00 0.00 0.00 3.86
6 7 4.874970 ACTGCTTGTATTGCTTTTTCTGG 58.125 39.130 0.00 0.00 0.00 3.86
7 8 6.672147 AGTACTGCTTGTATTGCTTTTTCTG 58.328 36.000 0.00 0.00 33.23 3.02
9 10 6.736853 CGTAGTACTGCTTGTATTGCTTTTTC 59.263 38.462 5.39 0.00 33.23 2.29
15 16 3.518590 ACCGTAGTACTGCTTGTATTGC 58.481 45.455 5.39 0.00 33.23 3.56
29 30 9.336171 CTACTATCTAGGAAAAAGTACCGTAGT 57.664 37.037 0.00 0.00 0.00 2.73
44 45 5.349270 CGCAGCAGTACTACTACTATCTAGG 59.651 48.000 0.00 0.00 31.46 3.02
58 59 2.526304 TGGATATTCCGCAGCAGTAC 57.474 50.000 0.00 0.00 40.17 2.73
63 64 3.141398 TCAGAAATGGATATTCCGCAGC 58.859 45.455 0.00 0.00 40.17 5.25
65 66 4.380531 GACTCAGAAATGGATATTCCGCA 58.619 43.478 0.00 0.00 40.17 5.69
83 84 2.559440 GGTGCTGATGAATCTGGACTC 58.441 52.381 17.09 7.67 43.24 3.36
92 93 0.321564 CTTGACCGGGTGCTGATGAA 60.322 55.000 3.30 0.00 0.00 2.57
151 152 4.881273 ACGCATCAAATTATCTACCAAGCA 59.119 37.500 0.00 0.00 0.00 3.91
152 153 5.007626 TCACGCATCAAATTATCTACCAAGC 59.992 40.000 0.00 0.00 0.00 4.01
153 154 6.258727 ACTCACGCATCAAATTATCTACCAAG 59.741 38.462 0.00 0.00 0.00 3.61
157 158 5.435557 GCACTCACGCATCAAATTATCTAC 58.564 41.667 0.00 0.00 0.00 2.59
159 160 3.001634 CGCACTCACGCATCAAATTATCT 59.998 43.478 0.00 0.00 0.00 1.98
228 231 4.415596 TGTCTGTTCTGGCCCAATTTATT 58.584 39.130 0.00 0.00 0.00 1.40
236 239 2.092323 GGTTTATGTCTGTTCTGGCCC 58.908 52.381 0.00 0.00 0.00 5.80
237 240 1.737793 CGGTTTATGTCTGTTCTGGCC 59.262 52.381 0.00 0.00 0.00 5.36
239 242 6.148811 ACATTTACGGTTTATGTCTGTTCTGG 59.851 38.462 2.98 0.00 0.00 3.86
262 265 6.546772 AGACAAATTTAGGGTCCGTAAAAACA 59.453 34.615 18.19 0.00 31.99 2.83
293 296 6.782082 TTGAACATCTGAGTAGCTCTATGT 57.218 37.500 0.00 9.97 38.45 2.29
296 299 9.973450 GATTATTTGAACATCTGAGTAGCTCTA 57.027 33.333 0.00 0.00 0.00 2.43
319 322 9.113876 CGTGAGAAGCGTTTTAAATTTTAGATT 57.886 29.630 0.00 0.00 0.00 2.40
324 327 5.038033 TGCGTGAGAAGCGTTTTAAATTTT 58.962 33.333 0.00 0.00 37.44 1.82
331 334 1.092921 TGGTGCGTGAGAAGCGTTTT 61.093 50.000 0.00 0.00 41.07 2.43
340 343 4.745125 ACGATAGATAATTTGGTGCGTGAG 59.255 41.667 0.00 0.00 41.38 3.51
421 426 3.315191 CGATTCGGTGCCCAAAATTATCT 59.685 43.478 0.00 0.00 0.00 1.98
422 427 3.628017 CGATTCGGTGCCCAAAATTATC 58.372 45.455 0.00 0.00 0.00 1.75
423 428 2.223711 GCGATTCGGTGCCCAAAATTAT 60.224 45.455 8.34 0.00 0.00 1.28
424 429 1.133407 GCGATTCGGTGCCCAAAATTA 59.867 47.619 8.34 0.00 0.00 1.40
425 430 0.108851 GCGATTCGGTGCCCAAAATT 60.109 50.000 8.34 0.00 0.00 1.82
427 432 1.602323 AGCGATTCGGTGCCCAAAA 60.602 52.632 10.37 0.00 35.85 2.44
436 441 0.249197 TGATCAGAGCAGCGATTCGG 60.249 55.000 8.34 0.00 0.00 4.30
470 505 0.475044 AACCACGGGGAAAACTGCTA 59.525 50.000 12.96 0.00 38.05 3.49
471 506 0.396556 AAACCACGGGGAAAACTGCT 60.397 50.000 12.96 0.00 38.05 4.24
472 507 0.031585 GAAACCACGGGGAAAACTGC 59.968 55.000 12.96 0.00 38.05 4.40
473 508 0.309612 CGAAACCACGGGGAAAACTG 59.690 55.000 12.96 0.00 38.05 3.16
474 509 0.107066 ACGAAACCACGGGGAAAACT 60.107 50.000 12.96 0.00 38.05 2.66
475 510 0.029700 CACGAAACCACGGGGAAAAC 59.970 55.000 12.96 0.00 38.05 2.43
476 511 0.107312 TCACGAAACCACGGGGAAAA 60.107 50.000 12.96 0.00 37.29 2.29
487 522 3.433274 TCACTTCATGCAGATCACGAAAC 59.567 43.478 0.00 0.00 0.00 2.78
497 532 6.659776 CATGTTATCTCATCACTTCATGCAG 58.340 40.000 0.00 0.00 0.00 4.41
498 533 6.613755 CATGTTATCTCATCACTTCATGCA 57.386 37.500 0.00 0.00 0.00 3.96
499 534 5.450171 GCATGTTATCTCATCACTTCATGC 58.550 41.667 10.20 10.20 45.71 4.06
500 535 6.613755 TGCATGTTATCTCATCACTTCATG 57.386 37.500 0.00 0.00 35.85 3.07
516 551 7.600231 TTATCCCAATCACATATTGCATGTT 57.400 32.000 0.00 0.00 0.00 2.71
517 552 7.069702 TGTTTATCCCAATCACATATTGCATGT 59.930 33.333 0.00 0.00 0.00 3.21
525 560 8.642935 TTTGACTTGTTTATCCCAATCACATA 57.357 30.769 0.00 0.00 0.00 2.29
541 576 0.475906 AGCTGGAGCCTTTGACTTGT 59.524 50.000 0.00 0.00 43.38 3.16
552 587 3.695606 TCGTGGTGGAGCTGGAGC 61.696 66.667 0.00 0.00 42.49 4.70
553 588 2.262915 GTCGTGGTGGAGCTGGAG 59.737 66.667 0.00 0.00 0.00 3.86
554 589 3.680786 CGTCGTGGTGGAGCTGGA 61.681 66.667 0.00 0.00 0.00 3.86
555 590 3.633094 CTCGTCGTGGTGGAGCTGG 62.633 68.421 0.00 0.00 0.00 4.85
556 591 2.126307 CTCGTCGTGGTGGAGCTG 60.126 66.667 0.00 0.00 0.00 4.24
656 691 0.103208 CAGAGCCGCCTTGTAGTAGG 59.897 60.000 0.00 0.00 38.40 3.18
712 752 1.898863 ATGGCCCACAAGATCTAGGT 58.101 50.000 0.00 0.00 0.00 3.08
715 755 2.694397 AGCTATGGCCCACAAGATCTA 58.306 47.619 0.00 0.00 39.73 1.98
801 841 1.076044 TGTACCGGTAGGGGGCTAC 60.076 63.158 16.41 3.39 43.47 3.58
811 851 2.203728 TGAGCCTGGTGTACCGGT 60.204 61.111 13.98 13.98 40.86 5.28
819 859 3.626924 GGGACACGTGAGCCTGGT 61.627 66.667 25.01 0.00 0.00 4.00
837 877 1.916777 CGGGGTTGGTGGTAGGAGT 60.917 63.158 0.00 0.00 0.00 3.85
838 878 2.987125 CGGGGTTGGTGGTAGGAG 59.013 66.667 0.00 0.00 0.00 3.69
839 879 3.324108 GCGGGGTTGGTGGTAGGA 61.324 66.667 0.00 0.00 0.00 2.94
840 880 4.770874 CGCGGGGTTGGTGGTAGG 62.771 72.222 0.00 0.00 0.00 3.18
841 881 4.770874 CCGCGGGGTTGGTGGTAG 62.771 72.222 20.10 0.00 0.00 3.18
922 965 6.830838 GGATTAAAGAATGATGAAGAGTGGGT 59.169 38.462 0.00 0.00 0.00 4.51
923 966 6.264067 GGGATTAAAGAATGATGAAGAGTGGG 59.736 42.308 0.00 0.00 0.00 4.61
924 967 6.264067 GGGGATTAAAGAATGATGAAGAGTGG 59.736 42.308 0.00 0.00 0.00 4.00
1376 1428 6.687105 GTCTAATACCATGAATCGCACAAAAC 59.313 38.462 0.00 0.00 0.00 2.43
1422 1474 1.990799 TCAAATCGCCTATATCGCCG 58.009 50.000 0.00 0.00 0.00 6.46
1478 1530 3.586100 ATACACGCAAAACCCCAAATC 57.414 42.857 0.00 0.00 0.00 2.17
1481 1533 1.269831 GCAATACACGCAAAACCCCAA 60.270 47.619 0.00 0.00 0.00 4.12
1519 1571 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
1521 1573 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
1571 1623 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
1572 1624 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
1573 1625 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
1574 1626 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
1575 1627 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
1576 1628 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1580 1632 9.458727 CAGATACTCCCTCCGTAAACTAATATA 57.541 37.037 0.00 0.00 0.00 0.86
1581 1633 7.949006 ACAGATACTCCCTCCGTAAACTAATAT 59.051 37.037 0.00 0.00 0.00 1.28
1582 1634 7.293073 ACAGATACTCCCTCCGTAAACTAATA 58.707 38.462 0.00 0.00 0.00 0.98
1583 1635 6.134754 ACAGATACTCCCTCCGTAAACTAAT 58.865 40.000 0.00 0.00 0.00 1.73
1584 1636 5.513233 ACAGATACTCCCTCCGTAAACTAA 58.487 41.667 0.00 0.00 0.00 2.24
1585 1637 5.121380 ACAGATACTCCCTCCGTAAACTA 57.879 43.478 0.00 0.00 0.00 2.24
1586 1638 3.978610 ACAGATACTCCCTCCGTAAACT 58.021 45.455 0.00 0.00 0.00 2.66
1587 1639 4.732672 AACAGATACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
1588 1640 5.163478 GCTAAACAGATACTCCCTCCGTAAA 60.163 44.000 0.00 0.00 0.00 2.01
1589 1641 4.340381 GCTAAACAGATACTCCCTCCGTAA 59.660 45.833 0.00 0.00 0.00 3.18
1590 1642 3.887716 GCTAAACAGATACTCCCTCCGTA 59.112 47.826 0.00 0.00 0.00 4.02
1591 1643 2.694109 GCTAAACAGATACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
1592 1644 2.959707 AGCTAAACAGATACTCCCTCCG 59.040 50.000 0.00 0.00 0.00 4.63
1593 1645 6.673839 AATAGCTAAACAGATACTCCCTCC 57.326 41.667 0.00 0.00 0.00 4.30
1620 1672 3.181434 TGAAACATGGCAAACCTCCTACT 60.181 43.478 0.00 0.00 36.63 2.57
1623 1675 2.242043 CTGAAACATGGCAAACCTCCT 58.758 47.619 0.00 0.00 36.63 3.69
1628 1680 2.865551 CCACAACTGAAACATGGCAAAC 59.134 45.455 0.00 0.00 0.00 2.93
1642 1694 1.529244 GCTCCCAACTGCCACAACT 60.529 57.895 0.00 0.00 0.00 3.16
1650 1702 1.003355 ATGTGACCGCTCCCAACTG 60.003 57.895 0.00 0.00 0.00 3.16
1781 1833 5.417811 TCAAATGCAGTCAAACACACATTT 58.582 33.333 0.00 0.00 41.33 2.32
1832 1884 1.475034 GGCAAGGTCCTATGATCGCAA 60.475 52.381 0.00 0.00 0.00 4.85
1874 1940 5.812286 ACTACGTAAACCCAAATTCTCCAT 58.188 37.500 0.00 0.00 0.00 3.41
1933 2000 2.224843 CCTATCCAACATGGCTGGCATA 60.225 50.000 16.84 0.96 37.47 3.14
2077 2144 1.073216 CGCTTGTAGTGCTCCGTCAG 61.073 60.000 0.00 0.00 0.00 3.51
2283 2350 2.609427 TGTAGATGATGCACTCCAGC 57.391 50.000 0.00 0.00 0.00 4.85
2375 2442 5.073554 AGGCATATGGATGATACAAGTTCCA 59.926 40.000 4.56 0.00 42.18 3.53
2379 2446 8.155620 AGATAAGGCATATGGATGATACAAGT 57.844 34.615 4.56 0.00 34.73 3.16
3011 3082 8.565896 AAGAAAAGAAAAATGCTTCCAACTTT 57.434 26.923 0.00 0.00 0.00 2.66
3205 3284 4.871993 AAATAGAGCAAGTGATCAAGCG 57.128 40.909 0.00 0.00 31.88 4.68
3270 3349 4.371855 TCAGCGTTTAGTAGATGGACTG 57.628 45.455 0.00 0.00 0.00 3.51
3286 3365 5.582550 TGTCATTCAGAACTACTATCAGCG 58.417 41.667 0.00 0.00 0.00 5.18
3360 3445 5.176406 CACATGTAAATCTAGACCAGCGATG 59.824 44.000 0.00 0.00 0.00 3.84
3387 3472 2.165641 TGCCTACTGTGTACCATCGAAG 59.834 50.000 0.00 0.00 0.00 3.79
3429 3514 6.034044 GCTGTGAACTGAAACTTACTATCTCG 59.966 42.308 0.00 0.00 0.00 4.04
3449 3534 2.857592 AAACAAGTTCAGCAGCTGTG 57.142 45.000 22.10 14.92 32.61 3.66
3489 3574 1.538047 TTTTCCTGCTTAGCTGCCTG 58.462 50.000 5.60 0.00 0.00 4.85
3599 3687 9.843334 ACGTTTTAAAACAGTCACTTTTTGATA 57.157 25.926 26.24 0.00 38.81 2.15
3604 3692 8.077386 TCAGAACGTTTTAAAACAGTCACTTTT 58.923 29.630 26.24 11.60 38.81 2.27
3639 3727 9.360093 CAGACTTAGTCAGTGAAGGTTTATAAG 57.640 37.037 15.23 0.00 35.01 1.73
3672 3760 8.311109 CCTTAGGTAGTGTTTGCCATTTATTTT 58.689 33.333 0.00 0.00 33.26 1.82
3677 3765 3.509967 GCCTTAGGTAGTGTTTGCCATTT 59.490 43.478 0.00 0.00 33.26 2.32
3693 3781 4.573900 ACAGTCACTTTCAGATGCCTTAG 58.426 43.478 0.00 0.00 0.00 2.18
3695 3783 3.498774 ACAGTCACTTTCAGATGCCTT 57.501 42.857 0.00 0.00 0.00 4.35
3753 3841 5.886960 AGGTTTACAAGCTAGCAATTCAG 57.113 39.130 18.83 2.13 37.49 3.02
3780 3868 6.961359 TGACCATGTGTCTAAAATTAGTCG 57.039 37.500 13.32 0.00 44.75 4.18
3783 3871 8.028354 TGCAATTGACCATGTGTCTAAAATTAG 58.972 33.333 10.34 0.00 44.75 1.73
3792 3880 4.445452 AGATTGCAATTGACCATGTGTC 57.555 40.909 14.33 7.22 44.72 3.67
3861 3949 5.231702 CCATTGATTCAGCATGTCAAAACA 58.768 37.500 0.00 0.00 35.20 2.83
4045 4133 3.066760 GTGGTTACTTGCAGCCAATATCC 59.933 47.826 0.00 0.00 29.81 2.59
4234 4342 5.102953 TCAGTTTTCAATCGATCAGGGAT 57.897 39.130 0.00 0.00 0.00 3.85
4281 4389 6.149129 TGAAGGTAGTAGCATACATGACAG 57.851 41.667 0.00 0.00 46.26 3.51
4297 4405 4.406003 GGAAGGAGTTAGATGCTGAAGGTA 59.594 45.833 0.00 0.00 0.00 3.08
4298 4406 3.198853 GGAAGGAGTTAGATGCTGAAGGT 59.801 47.826 0.00 0.00 0.00 3.50
4299 4407 3.454082 AGGAAGGAGTTAGATGCTGAAGG 59.546 47.826 0.00 0.00 0.00 3.46
4390 4499 0.615850 GCTTCTCCAGGTAAGCCAGT 59.384 55.000 14.90 0.00 41.80 4.00
4429 4538 1.004918 GAGAACCACCCTCACACCG 60.005 63.158 0.00 0.00 0.00 4.94
4601 4710 8.383175 TCCAGGATTATTTGTACCCTCATATTC 58.617 37.037 0.00 0.00 0.00 1.75
4725 4834 3.978855 CAGATTGAATGTAATGCATGGCG 59.021 43.478 0.00 0.00 37.96 5.69
4739 4848 5.034152 GCAAAAAGAACACGTCAGATTGAA 58.966 37.500 0.00 0.00 0.00 2.69
4784 4893 4.963318 ACCAAATCTTCTCTGTGTCTCA 57.037 40.909 0.00 0.00 0.00 3.27
4785 4894 4.453819 CCAACCAAATCTTCTCTGTGTCTC 59.546 45.833 0.00 0.00 0.00 3.36
4786 4895 4.103153 TCCAACCAAATCTTCTCTGTGTCT 59.897 41.667 0.00 0.00 0.00 3.41
4838 4950 3.687125 TGTTCGTGGGGTTGCAATTATA 58.313 40.909 0.59 0.00 0.00 0.98
4851 4963 8.915871 AAAAATATCTCATGAATTGTTCGTGG 57.084 30.769 10.91 4.00 44.79 4.94
4879 4991 7.960738 TGTTGAGTCAAAGTAAGAAGAAAAACG 59.039 33.333 7.25 0.00 0.00 3.60
4937 5049 5.452777 GTTTCAAAGACACTGCAGGTAATC 58.547 41.667 19.93 9.50 0.00 1.75
5044 5156 4.336713 TCATGTCGATCAGATTCTTCGAGT 59.663 41.667 10.03 1.67 42.01 4.18
5056 5168 6.426633 ACACACACTTAAAATCATGTCGATCA 59.573 34.615 0.00 0.00 31.11 2.92
5232 5347 6.036083 GCTCGCTCTAATGTTTTTAGTCATCA 59.964 38.462 0.00 0.00 0.00 3.07
5235 5350 4.630069 GGCTCGCTCTAATGTTTTTAGTCA 59.370 41.667 0.00 0.00 0.00 3.41
5241 5356 2.380084 TCGGCTCGCTCTAATGTTTT 57.620 45.000 0.00 0.00 0.00 2.43
5270 5385 9.348476 TCAATTCATAATTTCCGGACATGATAA 57.652 29.630 1.83 0.00 0.00 1.75
5272 5387 7.822161 TCAATTCATAATTTCCGGACATGAT 57.178 32.000 1.83 0.00 0.00 2.45
5386 5501 0.458669 GATTCCAAGTACGGCTCGGA 59.541 55.000 0.00 0.00 0.00 4.55
5387 5502 0.174845 TGATTCCAAGTACGGCTCGG 59.825 55.000 0.00 0.00 0.00 4.63
5388 5503 1.278238 GTGATTCCAAGTACGGCTCG 58.722 55.000 0.00 0.00 0.00 5.03
5411 5526 0.544697 GTATTTCCGGGCAGAGGGAA 59.455 55.000 0.00 0.00 40.44 3.97
5412 5527 0.326238 AGTATTTCCGGGCAGAGGGA 60.326 55.000 0.00 0.00 0.00 4.20
5413 5528 0.546598 AAGTATTTCCGGGCAGAGGG 59.453 55.000 0.00 0.00 0.00 4.30
5414 5529 1.065418 ACAAGTATTTCCGGGCAGAGG 60.065 52.381 0.00 0.00 0.00 3.69
5415 5530 2.280628 GACAAGTATTTCCGGGCAGAG 58.719 52.381 0.00 0.00 0.00 3.35
5416 5531 1.626321 TGACAAGTATTTCCGGGCAGA 59.374 47.619 0.00 0.00 0.00 4.26
5417 5532 2.107950 TGACAAGTATTTCCGGGCAG 57.892 50.000 0.00 0.00 0.00 4.85
5418 5533 2.026729 TGATGACAAGTATTTCCGGGCA 60.027 45.455 0.00 0.00 0.00 5.36
5419 5534 2.639065 TGATGACAAGTATTTCCGGGC 58.361 47.619 0.00 0.00 0.00 6.13
5420 5535 5.637006 TTTTGATGACAAGTATTTCCGGG 57.363 39.130 0.00 0.00 37.32 5.73
5421 5536 8.208718 TCTATTTTGATGACAAGTATTTCCGG 57.791 34.615 0.00 0.00 37.32 5.14


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.